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--- projects [2012/09/20 02:01] – jonathan
+++ projects [2015/08/11 21:02] – jarek
@@ Line 1: / Line 1: @@
-====== Currently offered Projects, Fall 2012 (updated September 5, 2012)  ======
+====== Proposed Projects for Fall 2015 ======
-(Listed in order received.)
+\\
-====== Continuation of a Path Diagram to Syntax Application ======
+=====Data visualization in Skydive=====
-**Supervisor**: Jeff Edmonds
+**Supervisor: Jarek Gryz**
-**Required Background**: General CSE408x prerequisites
+Skydive is a prototype system designed for database visualization using a concept of the so called
+data pyramid. The system is composed of three modules (DB - Database Module, D2I -
+Data-to-Image module, and VC - Visualizaton Client). Each is designed to use a different type
+of computer memory. The DB module uses disk to store and manage the raw data, and materialized
+data pyramids. The D2I module works with a small subset of the aggregated dataset,
+and stores data in main memory (RAM). The VC module uses the graphic card’s capabilities to
+perform more advanced operations – such as zooming, scaling, panning, and rotation – over the
+graphical representation of the data.
+Currently the system support three presentation models implemented within the Visualization
+Component, namely:
-**Recommended Background**: Java software development
+• a 2D heat-map;
-Structural equation modeling (SEM) is a statistical technique that is becoming increasingly popular in the educational and behavioral sciences. SEM allows researchers to test the validity of hypothesized models involving complex relationships among multiple variables. Collected data is used to estimate the parameters of the equations and assessing the fit of the model.
+• a 2.5 D heat-map by 3D barchart; and
-The software required is an application that allows researchers to define their hypothesized models visually and will output the correct syntax for the analytical software of their choosing.
+• a 2.5 D terrain (by mesh and UV-mapping).
-To date a promising functional application has been developed in JAVA by a Computer Science student as a 4080 project. The existing software allows the user to draw a path diagram and outputs code for the R package sem.  There are a number of improvements to be made (refinements and additions to graphical user interface) and then the application needs to be extended to output syntax appropriate for additional software applications (openMX, MPlus and EQS).  Though this project may not begin at “the first stages” of the software lifecycle, this scenario is likely common in the software development market. In addition, the student will be working with a primary “client” who is far less technically advanced, which is also reflective of real-world situations.
+The goal of the project is to implement two additional ways of data visualization as well as
+extend some of existing ones, that is:
-More details {{:continuation_of_a_path_diagram_to_syntax_application.pdf|here}}.
+. Implement and test functions for data pyramid-based visualization of time series.
-====== YUsend Thermal Vacuum (TVAC) Test Manager ======
+. Implement functions for visualization based on cross-product of data pyramids.
-**Supervisor**: Rob Allison (co-supervised with Hugh Chesser, Space Engineering)
+. Add support for specular and normal maps for 2.5 D terrain presentation model.
-**Required Background**: General CSE408x prerequisites, familiarity with C++ and Windows software tools
+Required Background: CSE 3421, Java programming course, (C programming course a plus)
-**Description** The YUsend (York University Space Engineering Nanosatellite Demonstration) Lab has procured a Windows XP-based industrial computer and temperature acquisition card (as well as other hardware) for performing TVAC testing of nanosatellites in the CSIL Lab (PSE 003). A “TVAC Test Manager” application written using LabView's G programming language will oversee the acquisition of temperatures (thermal test outputs) and control of IR lamps (thermal test inputs) during the rather long periods (4 or more days, 24 hours a day) of a TVAC test.
-Specific tasks include: 1. Writing temperature acquisition card (OMEGA Engineering CIO-DAS-Temp) drivers for LabView - should be written in Visual C++ or similar and compiled into SubVI format. 2. Write LabView VI's (“Virtual Instrument”) to perform (a) Test set-up activities - checkout of sensor and lamps, assigning neumonics to temperature sensors, setting of alarm conditions for sensors and lamps (b) Acquire and monitor temperature data and control lamp voltage during test, raise operator alarms for temperature or IR lamp anomalous conditions as required © Store temperature and control data for subsequent analysis and reporting. 3. (Optional) Interface the Test Manager with an orbital simulation tool which would be used to compute IR lamp inputs based on a simulation of the nanosatellite's orbital position and attitude (eg - in the sun, lamps on, in eclipse lamps off). The simulation tool is a package called Satellite Toolkit (STK) which has an TCP/IP-based API.
+\\
+=====Genome-wide identification of plant micro RNAs=====
-====== Game Playing Framework in Eiffel ======
+**Supervisor: Katalin Hudak**
-NO LONGER AVAILABLE
-**Supervisor**: Jonathan Ostroff
+The Hudak Lab in the Biology Department has an opening for a fourth-year Honours student to assist with a bioinformatics project. We study the pokeweed plant, Phytolacca americana, which displays broad-spectrum virus resistance. To evaluate pokeweed gene expression, we recently sequenced the plant’s mRNA and small RNA transcriptomes under jasmonic acid (JA) treatment. JA is a plant hormone that mediates defence against pathogens and insect herbivores. We are interested in learning how pokeweed gene expression is regulated by miRNAs during biotic stress.  Please note: no previous knowledge of biology is required.
-**Required Background**: Eiffel software development method
+Working with the support of a PhD student, your project will involve:
-**Description** Game playing frameworks in Eiffel such as Eiffelmedia usually wrap C frameworks in Eiffel. The goal of this project is to develop (initially, a simple) framework using pure Eiffel/EiffelVision so that the framework can be used on any platform (Windows, Linux, Mac) without external dependencies. Games provide a rich source for exploring object oriented software construction and design patterns, so that the framework would be useful in software design courses.
+) Prediction of micro RNA (miRNA) targets on the basis of complementary sequence matches
-====== Numerical Methods ======
+) Correlation of miRNA and mRNA expression changes to identify genes that are regulated by miRNAs
-**Supervisor**: Mike McNamee
+) Conducting pathway analysis to determine which biological processes are controlled by miRNAs
-**Required Background**: Good grade in a Numerical Methods course and good knowledge
+) Construction of a miRNA/target interaction network to visualize predictions
-of Fortran, C or similar language.
+This work will contribute to a scientific manuscript on miRNA-mediated gene regulation in pokeweed during response to JA.
-**Description**: Write, debug and run several Fortran programs related to solving
+Requirements:
-polynomial equations, with a view to comparing different known methods.
-====== Enabling SaaS access to an experimental AI planner ======
+) Pre-requisites as per EECS Calendar
-**Supervisor**: Sotirios Liaskos (liaskos at yorku dot ca)
+) Facility with script-writing/modification (in Perl or Python)
-**Required Background**: Good knowledge of Unix tools / Python, Perl or Awk. Comfort with algorithms and programming. Essential: 2031 -- Software Tools. Desired:
+) Preference for students with knowledge of statistics and familiarity with R programming
--- Functional & Logic Programming,
--- Design and Analysis of Algorithms,
--- Compilers and Interpreters.
-**Description**: This project involves enriching and integrating a set of fairly complex scripts, which are components of an Artificial Intelligence (AI) planner, and exporting them to the public in a Software-as-a-Service (SaaS) fashion.
+) Able to begin in September 2015
-The components are various Unix executables and LISP programs that need to interact in complex ways. The components may be residing in different servers in different universities. Currently integration is performed manually, at the expense of usability. Thus, we aim at constructing a module that: (a) integrates involved components to deliver output in one call, (b) exports a unique web interface (preferably following WSDL/SOAP) to be easily accessed by custom front-end tools by anyone, anywhere, (c ) offers a simple front-end for human users.
+Learning outcomes:
-Learning objectives:
+) Manipulate and analyze quantitative biological data
-  * Understand the technologies and process involved in turning native code into a web-service ("servicizing").
-  * Study a state-of-the-art AI planner and understand its workings.
-  * Exercise scripting skills.
+) Develop and test hypotheses by modifying existing software and writing new script
-====== Predicting Angular Error in Rigid Registration ======
+) Manage a CentOS computer server to store and facilitate ongoing research
-**Supervisor**: Burton Ma
+No knowledge of biology is required.
-**Description**: Registration is a fundamental step in image-based surgical
+For more information, please see:
-navigation. Several (seemingly) different approaches for predicting
+ Hudak Lab website- http://hudak.lab.yorku.ca/
-distance errors in registration are known, but for some surgical
-procedures, the angular error in registration is more important.
-This project will validate an approach for predicting angular
-error in registration; the student will use a combination of
-simulated and actual registration data for testing purposes.
-====== Calibration of a Tracked Pointer ======
+RNA sequencing- http://www.illumina.com/applications/sequencing/rna.html
-**Supervisor**: Burton Ma
+miRNAs- http://en.wikipedia.org/wiki/MicroRNA
-**Description**: Tracked pointers are the most common tools used in surgical
+\\
-navigation systems. A typical pointer has a tracked target on one
+=====Dynamic Interface Detection and Control Project=====
-end and a sharp or ball tip on the other end. Finding the location
-of the tip relative to the target is a calibration problem. One
-solution to the calibration problem involves pivoting the pointer
-about the tip while tracking the target; if the tip is kept
-stationary, then the target moves on the surface of a sphere.
-Fitting the tracking data to the surface of a sphere yields the
-location of the tip as the sphere center. Unfortunately, the
-calibrated tip position obtained using such a spherical calibration
-has high variance. This project will investigate how much variance
-there is in the calibrated tip position, and methods for reducing
-the variance of the calibrated tip position.
+**Supervisor: Michael Jenkin**
-====== A privacy safeguard framework for sharing photos on Facebook ======
-**Supervisor**: Uyen Trang Nguyen
+Contrary to most industries, fine chemical manufacturing is dominated by batch production methods. Increasing economic, environmental and safety pressures are motivating a turn towards continuous synthesis. Rather than making products in one big flask, continuous synthesis involves performing chemical reactions by flowing reagents through a tube. Working in this way provides more control over the reaction parameters leading to increases in product quality, and process efficiency and safety. The flow chemistry industry for fine chemical production is a relatively new but burgeoning field with a projected market capacity of billions of dollars by 2018.
+Extraction of the reaction mixture for purification and/or further processing is an important step in chemical manufacturing. This is a relatively straightforward operation in batch production, but offers several challenges for flowing processes. In order to facilitate continuous liquid extraction we require a sophisticated control system. This project involves designing, constructing and evaluating a pertinent practical problem in the field.
+A key step in the process takes place in a clear tube that is mounted vertically. The tube contains two fluids with a boundary between them. During the process material flows into and out of the tube from the top and the bottom. Chemical reactions take place within this tube and It is essential that the position of the boundary be monitored as its position in the tube is used to control the flow of materials into the tube.
+One way of solving this problem is to float a marker at the boundary between the two liquids and to monitor this boundary using a video camera. Although this approach solves the problem, it requires the introduction of a specific float within the tube. Can we build a system that monitors the boundary without resorting to the use of an artificial float?
+Specific goals of the project include:
+- Develop a computer vision system that can detect and monitor the interface between two miscible fluids of different density.
+- Evaluate the performance of the system over a range of different (and typical) fluids
+- Explore the use of different illuminant/filter choices to simplify the task for specific fluid combinations.
+The successful candidate(s) will have the experience of working with a diverse group of scientists and engineers toward the design and implementation of an automated liquid extraction device with applications across many industries. Upon successful prototyping, you will be able to interact with professionals in high-throughput manufacturing and system integration. Based on project success, you may be invited to join the MACOS(TM) team for implementation and process validation, which may involve opportunities in graduate school. You will have the opportunity to interact with the broad audience of MACOS(TM) technology including governmental regulatory agencies and industrial partners. This project will give you a great opportunity to apply your engineering expertise and gain experience in process implementation and technology transfer.
+For further information please contact,
+Michael Jenkin (jenkin@cse.yorku.ca) or Michal Organ (organ@yorku.ca)
+\\
+====== DDoS Attack using Google-bots ======
+**Supervisor**: Ntalija Vlajic
+**Recommended Background**: CSE 3213 or CSE 3214, CSE 3482
+Not long ago, botnets - networks of compromised computers - were seen as
+the most effective (if not the only) means of conducting Distributed Denial
+of Service (DDoS) attacks. However, with the growing popularity and prevalence
+of application-layer over other types of DDoS attacks, the DDoS execution
+landscape is becoming increasingly more diverse. An especially interesting
+new trend is the execution of application-layer DDoS attacks by means of
+skillfully manipulated Web-crawlers, such as Google-bots.
+The goal of this project is to design, implement and test a real-world
+framework consisting of the following: a) the attacker's web-accessible
+domain specially designed to attract Google-bots and then manipulate them
+into generating attack traffic towards the target/victim site; b) the
+victim's Web site set up in Amazon S3 cloud. In addition to the hands-on
+component, the project will also look into the statistical/numerical
+estimation of the framework's anticipated 'attack potential' relative
+to an actual (real-world) target/victim site.
+\\
+====== Attentive Sensing for Better Two-Way Communication in Remote Learning Environments ======
+**Supervisor**: James Elder
+**Required Background**: General CSE408x prerequisites, good programming skills,
+good math skills, knowledge of C and MATLAB programming languages
+One of the challenges in remote learning is to allow students to communicate effectively with the lecturer.  For example, when a student asks a question, communication will be more effective if the instructor has a zoomed view of the student’s face, so that s/he can interpret expressions etc.
+The goal of this project is to apply attentive sensing technology (www.elderlab.yorku.ca) to this problem.  This technology is able to monitor a large environment such as a classroom and direct a high-resolution ‘attentive’ sensor to events of interest.
+In particular, working with a senior graduate student or postdoctoral fellow, the  successful applicant will:
+  - Study the problem of detecting hand-raises in the preattentive sensor stream
+  - Implement algorithms for detecting hand-raises based upon this investigation
+  - Evaluate these algorithms in a real-classroom setting, using proprietary attentive sensing technology
+====== Attentive Sensing for Sport Video Recording Markets ======
+**Supervisor**: James Elder
+**Required Background**: Good programming skills; Good math skills; Knowledge of C and MATLAB programming languages
+The goal of this project is to modify York University’s patented attentive sensor technology to the sport video recording market.  Specific application domains under investigation include skiing, indoor BMX parks, and horse tracks.
+The general problem is to use attentive sensing technology (www.elderlab.yorku.ca) to visually detect and track multiple moving agents (e.g., skiers, riders, horses) and to select specific agents for active high-resolution smooth pursuit.
+The student will work with senior graduate students, postdoctoral fellows and research scientists to help modify the attentive sensing technology to operate in these domains.   Specific tasks include:
+.     Ground-truth available datasets
+.     Evaluate current attentive algorithms on these datasets
+.     Modify these algorithms to improve performance on these datasets
+------------
+\\
+====== Hunting for Bugs in Logging: applying JPF to log4j ======
+**Supervisor:** Franck van Breugel
+Description:
+Java PathFinder (JPF) is a tool that can detect bugs in Java code.
+The Java library Apache log4j allows developers to control which log
+statements are output.  In the past, Dickey et al. [1] have attempted
+to detect bugs in log4j by means of JPF with very limited succes.
+Recently, in collaboration with Shafiei (NASA) we have developed
+an extension of JPF called jpf-nhandler.  The aim of this project
+is to apply this extension to log4j.
+[1] David A. Dickey, B. Sinem Dorter, J. Michael German, Benjamin D. Madore, Mark W. Piper, Gabriel L. Zenarosa. "Evaluating Java PathFinder on Log4J."  2011.
+**Required Background:** General CSE408x prerequisites
+\\
+------------
+\\
+====== Mining Software Repositories Data======
+**Supervisor:** Zhen Ming (Jack) Jiang (zmjiang at cse dot yorku dot ca)
+**Required Background:** Good programming skills in Java; Good analytical and communication skills; Knowledge in AI and statistics; Interested in large scale software analysis
+**Short Description:** Software engineering data (e.g., source code repositories and bug databases) contains a wealth of information about a project's status and history. The research on Mining Software Repositories (MSR) aims to transform the data from static record-keeping repositories into knowledge, which can guide the software development process. For example, one can derive correct API usage patterns and flag anomalous (and potentially buggy) API usages by mining the source code across many projects in GitHub and Google Code. In this project, the student(s) will research and develop an efficient infrastructure, where MSR researchers and practitioners can share and analyze such data.
+\\
+------------------
+\\
+======Model-based Design and Development of Embedded Systems with Code Generation Tools======
+**Supervisor:** Jia Xu
+**Required Background:** At least a B+ in Embedded Systems (CSE3215), MATLAB, C programming skills, solid experience in using a microcontroller
+such as Arduino.
+**Project Description:**
+Model-based design with code generation tools can be used for simulation, rapid prototyping, and hardware-in-the-loop testing of embedded systems. This project explores model-based design and development of embedded systems on various hardware platforms with code generation tools. The selected student will develop and test embedded systems using model-based design and code generation tools such as MathWorks MATLAB /Simulink Coder.
+\\
+------------------
+\\
+======C2000 Concerto Microcontrollers======
+**Supervisor:** Jia Xu
+**Required Background:** At least a B+ in Embedded Systems (CSE3215),
+strong C programming skills, solid knowledge of microcontrollers
+**Description:** The C2000 Concerto family of microcontrollers combines
+two cores on a single-chip with on-chip low latency interprocessor communication between the two cores: a C28x 32-bit control core for
+real-time control with faster/more loops and small sampling window;
+and an ARM 32-bit Cortex-M3 host core for communications and general purpose. The selected student will evaluate the capabilities of the
+C2000 Concerto family of microcontrollers through testing and investigating open source software for real-time control applications
+that runs on C2000 Concerto Microcontrollers.
+\\
+------------------
+\\
+======Real-Time Bidding Platform======
+**Supervisor:** Jia Xu
+**Required Background:** At least a B+ in Operating System Fundamentals
+(CSE3221), strong Ubuntu/Linux, C++ programming, GCC, TCP/IP skills
+**Description:** Real-time bidding (RTB) is a new method of selling and buying online display advertising in real-time one ad impression at a time. Once a bid request has been sent out, all bids must be received within a strict deadline - generally under 100 milliseconds, including network latency. This project explores RTBkit, an open source SDK allowing developers to create customized real time ad bidding systems (for Media Buyers/Bidders).
+\\
+------------------
+\\
+======Circuit and Board Design for a Pulsed Ground Penetrating Radar======
+**Supervisor:**Sebastian Magierowski
-**Description**:
+**Description:** The project requires the construction of components for a ground penetrating radar.  The students would have to design microwave boards for the high-frequency components of this unit, on both the transmitter and the receiver.  On the transmitter side the board would take a 5-MHz input clock, run it through a series of off-the-shelf amplifiers and then through a shaping circuit that would convert the input into an outgoing series of pulses (still at 5-MHz repetition rate) less than 400-ps in duration each.  The bandwidth of the signal is roughly 2-8 GHz and hence requires very careful board layout.  The receiver would be a time-shifted sampler, used to sample the returning pulses in progressive periods.  This radar circuit is ultimately intended to be positioned on a rover doing ground analysis.
-One of the major privacy concerns in Online Social Networks is photo sharing.  A user may post his/her friends’ photos without their consent.  The friends have no control over the user’s Facebook activities, namely photo sharing.  In this project, we design and implement a third-party Facebook application that allows people to protect their identities in photos uploaded by another user without their consent.
-**Required prerequisite background**:  Proficiency in programming, especially in Java and Web application programming.
+**Required Background** A background in undergraduate-level electronics is very important.  Experience with board level implementations and knowledge of microstrip lines would be helpful, otherwise the basics would have to be picked up during the project.
-**Desired prerequisite**: Knowledge of image processing, Facebook API, JavaScript Object Notation (JSON)
+\\
+------------------
+\\
+More project proposals may be added here in the first week of the winter term.
+\\
+------------------
+\\
+\\